ソフトウェア | 名称 | バージョン | 分類 |
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REFMAC | 5.8.0352精密化 | XDS | | データ削減 | Aimless | | データスケーリング | PHASER | | 位相決定 | |
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精密化 | 構造決定の手法: 分子置換 開始モデル: 4NYQ 解像度: 2.1→37.012 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.06 / SU ML: 0.225 / 交差検証法: FREE R-VALUE / ESU R: 0.277 / ESU R Free: 0.216 / 詳細: Hydrogens have been added in their riding positions
| Rfactor | 反射数 | %反射 |
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Rfree | 0.2523 | 433 | 5.095 % |
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Rwork | 0.1962 | 8065 | - |
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all | 0.199 | - | - |
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obs | - | 8498 | 96.689 % |
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK BULK SOLVENT |
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原子変位パラメータ | Biso mean: 40.13 Å2
| Baniso -1 | Baniso -2 | Baniso -3 |
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1- | -2.312 Å2 | 1.22 Å2 | 0.946 Å2 |
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2- | - | -0.371 Å2 | 2.202 Å2 |
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3- | - | - | 0.257 Å2 |
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精密化ステップ | サイクル: LAST / 解像度: 2.1→37.012 Å
| タンパク質 | 核酸 | リガンド | 溶媒 | 全体 |
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原子数 | 1221 | 0 | 42 | 7 | 1270 |
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拘束条件 | Refine-ID | タイプ | Dev ideal | Dev ideal target | 数 |
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X-RAY DIFFRACTION | r_bond_refined_d0.015 | 0.012 | 1306 | X-RAY DIFFRACTION | r_bond_other_d0.003 | 0.016 | 1145 | X-RAY DIFFRACTION | r_angle_refined_deg2.597 | 1.691 | 1782 | X-RAY DIFFRACTION | r_angle_other_deg0.862 | 1.578 | 2680 | X-RAY DIFFRACTION | r_dihedral_angle_1_deg8.106 | 5 | 148 | X-RAY DIFFRACTION | r_dihedral_angle_2_deg11.601 | 5 | 6 | X-RAY DIFFRACTION | r_dihedral_angle_3_deg17.61 | 10 | 199 | X-RAY DIFFRACTION | r_dihedral_angle_6_deg17.18 | 10 | 59 | X-RAY DIFFRACTION | r_chiral_restr0.124 | 0.2 | 195 | X-RAY DIFFRACTION | r_gen_planes_refined0.014 | 0.02 | 1445 | X-RAY DIFFRACTION | r_gen_planes_other0.001 | 0.02 | 266 | X-RAY DIFFRACTION | r_nbd_refined0.221 | 0.2 | 240 | X-RAY DIFFRACTION | r_symmetry_nbd_other0.216 | 0.2 | 1119 | X-RAY DIFFRACTION | r_nbtor_refined0.204 | 0.2 | 624 | X-RAY DIFFRACTION | r_symmetry_nbtor_other0.102 | 0.2 | 708 | X-RAY DIFFRACTION | r_xyhbond_nbd_refined0.193 | 0.2 | 29 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_other0.087 | 0.2 | 1 | X-RAY DIFFRACTION | r_symmetry_nbd_refined0.272 | 0.2 | 11 | X-RAY DIFFRACTION | r_nbd_other0.252 | 0.2 | 43 | X-RAY DIFFRACTION | r_symmetry_xyhbond_nbd_refined0.138 | 0.2 | 2 | X-RAY DIFFRACTION | r_mcbond_it4.785 | 3.428 | 598 | X-RAY DIFFRACTION | r_mcbond_other4.786 | 3.429 | 598 | X-RAY DIFFRACTION | r_mcangle_it6.674 | 5.116 | 744 | X-RAY DIFFRACTION | r_mcangle_other6.672 | 5.123 | 745 | X-RAY DIFFRACTION | r_scbond_it7.909 | 4.522 | 708 | X-RAY DIFFRACTION | r_scbond_other7.903 | 4.524 | 709 | X-RAY DIFFRACTION | r_scangle_it11.815 | 6.412 | 1038 | X-RAY DIFFRACTION | r_scangle_other11.81 | 6.413 | 1039 | X-RAY DIFFRACTION | r_lrange_it14.139 | 51.75 | 1405 | X-RAY DIFFRACTION | r_lrange_other14.135 | 51.793 | 1406 | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20 解像度 (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Rfactor all | Num. reflection all | Fsc free | Fsc work | % reflection obs (%) | WRfactor Rwork |
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2.1-2.154 | 0.299 | 31 | 0.289 | 592 | 0.29 | 652 | 0.934 | 0.938 | 95.5521 | 0.291 | 2.154-2.213 | 0.439 | 25 | 0.256 | 568 | 0.263 | 624 | 0.869 | 0.952 | 95.0321 | 0.256 | 2.213-2.277 | 0.305 | 28 | 0.261 | 567 | 0.263 | 619 | 0.931 | 0.949 | 96.1228 | 0.255 | 2.277-2.347 | 0.246 | 22 | 0.245 | 560 | 0.245 | 610 | 0.961 | 0.957 | 95.4098 | 0.242 | 2.347-2.424 | 0.327 | 19 | 0.248 | 545 | 0.251 | 576 | 0.921 | 0.957 | 97.9167 | 0.243 | 2.424-2.508 | 0.284 | 24 | 0.237 | 503 | 0.239 | 552 | 0.935 | 0.959 | 95.471 | 0.238 | 2.508-2.603 | 0.345 | 28 | 0.206 | 497 | 0.213 | 536 | 0.915 | 0.971 | 97.9478 | 0.207 | 2.603-2.708 | 0.269 | 43 | 0.2 | 479 | 0.205 | 542 | 0.961 | 0.973 | 96.31 | 0.21 | 2.708-2.828 | 0.313 | 27 | 0.203 | 428 | 0.21 | 465 | 0.929 | 0.971 | 97.8495 | 0.213 | 2.828-2.965 | 0.264 | 21 | 0.153 | 465 | 0.157 | 499 | 0.959 | 0.986 | 97.3948 | 0.163 | 2.965-3.125 | 0.208 | 28 | 0.168 | 396 | 0.171 | 433 | 0.975 | 0.983 | 97.9215 | 0.18 | 3.125-3.313 | 0.239 | 30 | 0.167 | 402 | 0.172 | 443 | 0.96 | 0.983 | 97.5169 | 0.187 | 3.313-3.539 | 0.226 | 31 | 0.155 | 367 | 0.161 | 405 | 0.96 | 0.987 | 98.2716 | 0.177 | 3.539-3.82 | 0.18 | 8 | 0.154 | 350 | 0.155 | 368 | 0.987 | 0.987 | 97.2826 | 0.175 | 3.82-4.18 | 0.205 | 20 | 0.158 | 326 | 0.161 | 359 | 0.974 | 0.984 | 96.3788 | 0.184 | 4.18-4.666 | 0.186 | 13 | 0.145 | 288 | 0.147 | 313 | 0.982 | 0.986 | 96.1661 | 0.168 | 4.666-5.374 | 0.248 | 11 | 0.187 | 248 | 0.19 | 271 | 0.978 | 0.982 | 95.572 | 0.225 | 5.374-6.547 | 0.258 | 4 | 0.208 | 232 | 0.209 | 243 | 0.908 | 0.978 | 97.1193 | 0.249 | 6.547-9.117 | 0.291 | 9 | 0.243 | 157 | 0.246 | 170 | 0.98 | 0.97 | 97.6471 | 0.302 | 9.117-37.012 | 0.202 | 11 | 0.254 | 94 | 0.248 | 108 | 0.984 | 0.947 | 97.2222 | 0.31 |
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